An osteolytic lesion with a small central area of mineralization and sclerotic borders was discovered incidentally in the clivus on the cone-beam computed tomography (CBCT) of a 27-year-old male patient. This benign appearance indicated a primary differential diagnosis of non-aggressive lesions such as fibro-osseous lesions and arrested pneumatization. Further, on magnetic resonance imaging (MRI), the lesion showed a homogenously low T1 signal intensity with mild internal enhancement after post-gadolinium and a heterogeneous T2 signal intensity. These signal characteristics might be attributed to the fibrous tissues, chondroid matrix, calcific material, or cystic component of the lesion; thus, chondroblastoma and chondromyxoid fibroma were added to the differential diagnosis. Although this report was limited by the lack of final diagnosis and the patient lost to follow-up, the incidental skull base finding would be important for interpreting the entire volume of CBCT by a qualified oral and maxillofacial radiologist.